Dear Diels & Alder,

Oh, Diels-Alder reaction, it was love at first sight. I saw your cute mechanism and knew it was meant to be. Ever since that day you have been my favorite organic chemistry reaction. The more I learned about you, the more fun you were to me. Here is why…

Love,

Jacqueline

It is possible that many of you read that paragraph and it brought back some horrible memories of arrows, lines, hours of horrendous studying, and confusion. However, organic chemistry to me was an exciting course consisting of various chemical puzzles (see end of post for your chance to solve). Believe it or not, I really did fall in love and it is one reason why I spent the last six years since that glorious course becoming a physical organic chemist.

I thought it would be fun to do some organic chemistry basics. It is an undergraduate course required for many science majors and professions including medicine, biology, and engineering. I know, I know many people dread, hate, or fail the course. However, here is a fun introduction and Diels-Alder puzzles at the end for you problem solvers.

Organic chemistry examines carbon-based chemistry. Carbon, generally, makes four covalent bonds. Covalent bonds are when two atoms share a pair of electrons. Carbon, one of the sluttiest chemical elements, usually wants to share its valence electrons. Valence electrons are defined as electrons available to participate in chemical bonding.

The first barrier to understanding the complex subject is to comprehend the ‘line notation’ used to draw the compounds. Below I show the four-carbon compound, butane. Each of the vertices is a carbon that is fully saturated with hydrogen atoms. This is how the line notation translates to a fully drawn structure.

Multiple chemical bonds can also be drawn using line notation. Counting the carbon-carbon bonds allows you determine the number of hydrogens required to fully saturate the hydrocarbon.

With the basics aside, let’s take a closer look at the Diels-Alder reaction. If you have taken an organic chemistry course, then you are probably familiar with this reaction or have forgotten it amidst the many named reactions you were forced to remember. This reaction is a cycloaddition. A cycloaddition is where two components, in this case a diene and a dienophile, add together to form a cyclic compound. A diene has two carbon double bonds, in the case of the Diels-Alder reaction it has to be a conjugated diene (alternating double bonds). As the name might suggest, a dienophile ‘loves’ to react with a diene. However, the requirement of a dienophile is that it has one carbon-carbon double bond.

Electron movement is depicted by arrows in organic mechanisms. Electrons move from the arrow end to where the arrow is pointed.

The diene and dienophile undergo a reaction to form a six-membered ring. The Diels-Alder reaction simultaneously moves six electrons to form cyclohexene. Diels and Alder won the Nobel prize for this elegant reaction in 1950. Even today it is used in many synthetic reactions and in drug design, as it is one of the best ways to form the cyclohexene compound.

Puzzle Time! I am going to give the folks still interested two puzzles to work out on their own. The second will be more difficult than the first. (They are intended for an organic chemistry novice or someone who likes to think in 3D.)

Puzzle 1: Here are the reactants and product of a Diels-Alder reaction. Predict where the arrows should be drawn.

Puzzle 2: Here are the reactants of a Diels-Alder reaction. Predict the arrows and product. Use Puzzle 1 as a hint to predict the product.

The answers are easily found by googling. If requested in the comments, I will post the answers to the puzzles next week.

Jacqueline, a true Floridian, wandered up to the tundra of Athens, Georgia to receive her PhD in computational quantum chemistry. Returning to her roots, she is currently working as a postdoctoral researcher in Tampa in the field of computational biochemistry investigating the wonders of penicillin-like drugs. When she is not slaving over the computer, her varied interests include international travel, Brazilian jiu jitsu, kickboxing, fancy food, (American) football, and Belgian quadrupels. She is also the founder of EligibleReceiver.com, a football blog with an exclusive female writing staff. Check out her sports ramblings there or follow her on Twitter @jhargis9.

I just finished up my first organic chemistry course – and my first chem course at all in something like 8 years. I took it as a component of my PhD minor, which since I’m doing Bioinformatics I thought would be relevant.

I, too, ADORED the organic chemistry classes I took a couple of years ago. They were challenging (O Chem 1 was the first class I received anything less than a straight A), but the puzzle aspect was wonderful. In the second semester I made myself a set of cards and played a sort of “O Chem Solitaire” to study, randomly making different chemicals and then trying to figure out how I could get the second chemical from the first using the reactions we learned in class.

This is a wonderful reaction. I took a course last semester in computational chemistry where we calculated the properties of the ‘Puzzle 2’ reaction in Gaussian. We looked at the HOMO LUMO interactions; IR spectra; activation barriers and reaction enthalpies.